bella-companion 0.0.12__tar.gz → 0.0.14__tar.gz

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  1. {bella_companion-0.0.12 → bella_companion-0.0.14}/PKG-INFO +2 -2
  2. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/run_beast.py +4 -2
  3. {bella_companion-0.0.12 → bella_companion-0.0.14}/pyproject.toml +2 -2
  4. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/__init__.py +0 -0
  5. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/cli.py +0 -0
  6. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/__init__.py +0 -0
  7. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/__pycache__/run_beast.cpython-311.pyc +0 -0
  8. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/__pycache__/run_mlp.cpython-311.pyc +0 -0
  9. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/__pycache__/run_nonparametric.cpython-311.pyc +0 -0
  10. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/__pycache__/summarize_logs.cpython-311.pyc +0 -0
  11. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/data/change_times.csv +0 -0
  12. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/data/traits.csv +0 -0
  13. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/data/trees.nwk +0 -0
  14. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/results.py +0 -0
  15. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/summarize_logs.py +0 -0
  16. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/__init__.py +0 -0
  17. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/__pycache__/__init__.cpython-310.pyc +0 -0
  18. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/__pycache__/__init__.cpython-311.pyc +0 -0
  19. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/__pycache__/features.cpython-310.pyc +0 -0
  20. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/__pycache__/features.cpython-311.pyc +0 -0
  21. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/__pycache__/generate_data.cpython-310.pyc +0 -0
  22. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/__pycache__/generate_data.cpython-311.pyc +0 -0
  23. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/__pycache__/run_beast.cpython-311.pyc +0 -0
  24. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/__pycache__/summarize_logs.cpython-311.pyc +0 -0
  25. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/features.py +0 -0
  26. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__init__.py +0 -0
  27. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/__init__.cpython-311.pyc +0 -0
  28. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/epi_explainations.cpython-311.pyc +0 -0
  29. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/epi_predictions.cpython-311.pyc +0 -0
  30. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/epi_simulations.cpython-311.pyc +0 -0
  31. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/fbd_explainations.cpython-311.pyc +0 -0
  32. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/fbd_predictions.cpython-311.pyc +0 -0
  33. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/fbd_simulations.cpython-311.pyc +0 -0
  34. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/figure1.cpython-311.pyc +0 -0
  35. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/plot.cpython-311.pyc +0 -0
  36. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/scenarios.cpython-311.pyc +0 -0
  37. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/__pycache__/utils.cpython-311.pyc +0 -0
  38. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/epi_multitype_results.py +0 -0
  39. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/epi_skyline_results.py +0 -0
  40. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/explain/__init__.py +0 -0
  41. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/explain/pdp.py +0 -0
  42. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/explain/shap.py +0 -0
  43. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/fbd_2traits_results.py +0 -0
  44. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/fbd_no_traits_results.py +0 -0
  45. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/scenarios.py +0 -0
  46. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/figures/utils.py +0 -0
  47. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/generate_data.py +0 -0
  48. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/generate_figures.py +0 -0
  49. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/metrics.py +0 -0
  50. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/run_beast.py +0 -0
  51. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__init__.py +0 -0
  52. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/__init__.cpython-310.pyc +0 -0
  53. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/__init__.cpython-311.pyc +0 -0
  54. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/common.cpython-310.pyc +0 -0
  55. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/common.cpython-311.pyc +0 -0
  56. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-310.pyc +0 -0
  57. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-311.pyc +0 -0
  58. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-310.pyc +0 -0
  59. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-311.pyc +0 -0
  60. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-310.pyc +0 -0
  61. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-311.pyc +0 -0
  62. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-310.pyc +0 -0
  63. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-311.pyc +0 -0
  64. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/scenario.cpython-310.pyc +0 -0
  65. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/scenario.cpython-311.pyc +0 -0
  66. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/__pycache__/utils.cpython-311.pyc +0 -0
  67. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/common.py +0 -0
  68. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/epi_multitype.py +0 -0
  69. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/epi_skyline.py +0 -0
  70. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/fbd_2traits.py +0 -0
  71. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/fbd_no_traits.py +0 -0
  72. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/scenarios/scenario.py +0 -0
  73. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/simulations/summarize_logs.py +0 -0
  74. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/utils/__init__.py +0 -0
  75. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/utils/beast.py +0 -0
  76. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/utils/explain.py +0 -0
  77. {bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/utils/slurm.py +0 -0
{bella_companion-0.0.12 → bella_companion-0.0.14}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: bella-companion
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- Version: 0.0.12
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+ Version: 0.0.14
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  Summary:
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  Author: gabriele-marino
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  Author-email: gabmarino.8601@gmail.com
@@ -10,7 +10,7 @@ Classifier: Programming Language :: Python :: 3.10
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  Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
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  Requires-Dist: arviz (>=0.22.0,<0.23.0)
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- Requires-Dist: bella-lumiere (>=0.0.13,<0.0.14)
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+ Requires-Dist: bella-lumiere (>=0.0.14,<0.0.15)
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  Requires-Dist: dotenv (>=0.9.9,<0.10.0)
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  Requires-Dist: phylogenie (>=2.1.30,<3.0.0)
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  Requires-Dist: seaborn (>=0.13.2,<0.14.0)
{bella_companion-0.0.12 → bella_companion-0.0.14}/bella_companion/fbd_empirical/run_beast.py RENAMED
@@ -1,6 +1,6 @@
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  import json
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  import os
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- from itertools import combinations
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+ from itertools import product
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  from pathlib import Path
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  import numpy as np
@@ -14,7 +14,9 @@ from bella_companion.utils import submit_job
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  def _get_migration_rates_init(types: list[str], init_rate: float = 1) -> str:
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  mus: list[float] = []
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- for t1, t2 in combinations(types, 2):
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+ for t1, t2 in product(types, types):
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+ if t1 == t2:
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+ continue
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  traits1 = np.array(list(map(int, t1.split("_"))))
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  traits2 = np.array(list(map(int, t2.split("_"))))
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  mus.append(init_rate if np.sum(np.abs(traits1 - traits2)) == 1 else 0)
{bella_companion-0.0.12 → bella_companion-0.0.14}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "bella-companion"
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- version = "0.0.12"
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+ version = "0.0.14"
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  description = ""
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  authors = ["gabriele-marino <gabmarino.8601@gmail.com>"]
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@@ -8,7 +8,7 @@ authors = ["gabriele-marino <gabmarino.8601@gmail.com>"]
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  python = "^3.10"
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  arviz = "^0.22.0"
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- bella-lumiere = "^0.0.13"
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+ bella-lumiere = "^0.0.14"
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  dotenv = "^0.9.9"
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  phylogenie = "^2.1.30"
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  seaborn = "^0.13.2"